In 1993, Kirshner played a dominatrix in Denys Arcand's Love and Human Remains and won a Genie nomination for Best Performance by an Actress in a Supporting Role. The following year, she starred in Atom Egoyan's Exotica. In 1996, she appeared in The Crow: City of Angels.

Kirshner appeared in the first three episodes of 24 as bisexual assassin Mandy in 2001. She would later reprise the role for the second season's finale and in the latter half of the show's fourth season. Also in 2001, Kirshner played Catherine Wyler, The Cruelest Girl in School, in Not Another Teen Movie. The character is primarily a spoof of Kathryn Merteuil (played by Sarah Michelle Gellar) in Cruel Intentions, and partially based on Mackenzie Siler from She's All That. In Marilyn Manson's music video for "Tainted Love", which was featured on the movie's soundtrack, she makes a cameo appearance as her character Catherine Wyler.

In 2004, Kirshner was cast as author Jenny Schecter, a lesbian main character in the drama series The L Word for the show's six seasons through 2009. In 2006, she starred in Brian De Palma's The Black Dahlia, alongside Josh Hartnett, Aaron Eckhart, Scarlett Johansson and Hilary Swank. Kirshner plays a young aspiring actress, Elizabeth Short, who was mysteriously mutilated and murdered in 1947.

• "The L Word" .... Jenny Schecter (70 episodes, 2004-2009)
       - Last Word (2009) TV episode .... Jenny Schecter
       - Last Couple Standing (2009) TV episode .... Jenny Schecter
       - Lactose Intolerant (2009) TV episode .... Jenny Schecter
       - Litmus Test (2009) TV episode .... Jenny Schecter
       - Leaving Los Angeles (2009) TV episode .... Jenny Schecter
        (65 more)
• Miss Conception (2008) .... Clem
  ... aka Last Minute Baby (Germany: TV title)
  ... aka Miss Conception (USA: new title)
• They Come Back (2007) (TV) .... Faith Hardy
• The Black Dahlia (2006) .... Elizabeth Short
  ... aka Black Dahlia (Germany)
  ... aka Die Schwarze Dahlie (Germany: TV title)
• 24: The Game (2006) (VG) (voice) (uncredited) .... Mandy
• "24" .... Mandy (7 episodes, 2001-2005)
       - Day 4: 5:00 a.m.-6:00 a.m. (2005) TV episode .... Mandy
       - Day 4: 6:00 a.m.-7:00 a.m. (2005) TV episode .... Mandy
       - Day 4: 4:00 a.m.-5:00 a.m. (2005) TV episode (uncredited) .... Mandy
       - Day 2: 7:00 a.m.-8:00 a.m. (2003) TV episode (uncredited) .... Mandy
       - 2:00 a.m.-3:00 a.m. (2001) TV episode .... Mandy
        (2 more)
• The Iris Effect (2004) .... Rebecca
  ... aka Exile (Russia)
• Party Monster (2003) .... Natasha
• Now & Forever (2002) .... Angela Wilson
• "Wolf Lake" .... Ruby Cates / ... (4 episodes, 2001-2002)
       - Legend of Lost Lenore (2002) TV episode .... Ruby Wilder/Ruby Cates
       - Tastes Like Chicken (2001) TV episode .... Ruby Wilder/Ruby Cates
       - Soup to Nuts (2001) TV episode .... Ruby Wilder/Ruby Cates
       - The Changing (2001) TV episode .... Ruby Wilder/Ruby Cates
• New Best Friend (2002) .... Alicia Campbell
• Not Another Teen Movie (2001) .... Catherine Wyler
  ... aka Sex Academy (Europe: English title: new title)
• According to Spencer (2001) .... Melora
  ... aka Der Pechvogel (Germany: new title)
  ... aka Garage Sale
• Century Hotel (2001) .... Dominique
• Cowboys and Angels (2000) .... Candice